Molecular phylogeny of leader proteinase gene of type A of Foot-and-mouth disease virus from India

Molecular phylogeny of leader proteinase gene of type A of Foot-and-mouth disease virus from India We previously demonstrated the presence of three genotypes (IV, VI and VII) of type A (subtype A22) of Foot-and-mouth disease virus (FMDV) in India based on 1D gene sequence analysis. In the present study, the leader proteinase (L pro ) gene sequences of 35 type A FMDV field isolates sampled over a period of 24 years (1977–2000) have been analyzed. Maximum-likelihood (ML) phylogenetic analysis revealed four distinct genetic lineages (A–D), indicating high divergence in L gene of type A FMDV. Lineages A and D correspond to the earlier genotypes IV, and VII, respectively. The genotype VI isolates were divided into two separate lineages (B and C) in the tree with high confidence values (96–99%). One isolate (IND 21/90) showed incongruous grouping between the (1D and L) gene-based analyses, which could be due to intergenotypic recombination. The ML molecular clock hypothesis was easily rejected on the data set studied indicating the absence of clock-like evolution in the L gene. ML codon-substitution models identified positive selection in the amino acid site 194 of C-terminal extension of the Lb pro with high posterior probability (>99%). The catalytic triad of the L pro at C-51, H-148 and D-163 were conserved across all the Indian isolates studied. Finally, amino acid differences between the lineages have been discussed briefly. Archives of Virology Springer Journals

Molecular phylogeny of leader proteinase gene of type A of Foot-and-mouth disease virus from India

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